Genetic association studies under the population stratification, family pedigree and application to genome-wide association studies

This dissertation has three separate parts: the first part deals with the general pedigree association testing incorporating continuous covariates; the second part deals with the association tests under population stratification using the conditional likelihood tests; the third part deals with the genome-wide association studies based on the real rheumatoid arthritis (RA) disease data sets from Genetic Analysis Workshop 16 (GAW16) problem 1. Many statistical tests are developed to test the linkage and association using either case-control status or phenotype covariates for family data structure, separately. Those univariate analyses might not use all the information coming from the family members in practical studies. On the other hand, the human complex disease do not have a clear inheritance pattern, there might exist the gene interactions or act independently. In part I, the new proposed approach MPDT is focused on how to use both the case control information as well as the phenotype covariates. This approach can be applied to detect multiple marker effects. Based on the two existing popular statistics in family studies for case-control and quantitative traits respectively, the new approach could be used in the simple family structure data set as well as general pedigree structure. The combined statistics are calculated using the two statistics; A permutation procedure is applied for assessing the p-value with adjustment from the Bonferroni for the multiple markers. We use simulation studies to evaluate the type I error rates and the powers of the proposed approach. Our results show that the combined test using both case-control information and phenotype covariates not only has the correct type I error rates but also is more powerful than the other existing methods. For multiple marker interactions, our proposed method is also very powerful. Selective genotyping is an economical strategy in detecting and mapping quantitative trait loci in the genetic dissection of complex disease. When the samples arise from different ethnic groups or an admixture population, all the existing selective genotyping methods may result in spurious association due to different ancestry distributions. The problem can be more serious when the sample size is large, a general requirement to obtain sufficient power to detect modest genetic effects for most complex traits. In part II, I describe a useful strategy in selective genotyping while population stratification is present. Our procedure used a principal component based approach to eliminate any effect of population stratification. The paper evaluates the performance of our procedure using both simulated data from an early study data sets and also the HapMap data sets in a variety of population admixture models generated from empirical data. There are one binary trait and two continuous traits in the rheumatoid arthritis dataset of Problem 1 in the Genetic Analysis Workshop 16 (GAW16): RA status, AntiCCP and IgM. To allow multiple traits, we suggest a set of SNP-level F statistics by the concept of multiple-correlation to measure the genetic association between multiple trait values and SNP-specific genotypic scores and obtain their null distributions. Hereby, we perform 6 genome-wide association analyses using the novel one- and two-stage approaches which are based on single, double and triple traits. Incorporating all these 6 analyses, we successfully validate the SNPs which have been identified to be responsible for rheumatoid arthritis in the literature and detect more disease susceptibility SNPs for follow-up studies in the future. Except for chromosome 13 and 18, each of the others is found to harbour susceptible genetic regions for rheumatoid arthritis or related diseases, i.e., lupus erythematosus. This topic is discussed in part III.

Population transcriptomics of life-history variation in the genus Salmo

In this study, we demonstrate the power of applying complementary DNA (cDNA) microarray technology to identifying candidate loci that exhibit subtle differences in expression levels associated with a complex trait in natural populations of a nonmodel organism. Using a highly replicated experimental design involving 180 cDNA microarray experiments, we measured gene-expression levels from 1098 transcript probes in 90 individuals originating from six brown trout (Salmo trutta) and one Atlantic salmon (Salmo salar) population, which follow either a migratory or a sedentary life history. We identified several candidate genes associated with preparatory adaptations to different life histories in salmonids, including genes encoding for transaldolase 1, constitutive heat-shock protein HSC70-1 and endozepine. Some of these genes clustered into functional groups, providing insight into the physiological pathways potentially involved in the expression of life-history related phenotypic differences. Such differences included the down-regulation of genes involved in the respiratory system of future migratory individuals. In addition, we used linear discriminant analysis to identify a set of 12 genes that correctly classified immature individuals as migratory or sedentary with high accuracy. Using the expression levels of these 12 genes, 17 out of 18 individuals used for cross-validation were correctly assigned to their respective life-history phenotype. Finally, we found various candidate genes associated with physiological changes that are likely to be involved in preadaptations to seawater in anadromous populations of the genus Salmo, one of which was identified to encode for nucleophosmin 1. Our findings thus provide new molecular insights into salmonid life-history variation, opening new perspectives in the study of this complex trait.

Clinical experience with the use of bivalirudin in a large population undergoing endovascular abdominal aortic aneurysm repair

PURPOSE: To retrospectively evaluate the safety and effectiveness of the use of bivalirudin, a direct thrombin antagonist, compared with unfractionated heparin in endovascular aneurysm repair (EVAR). MATERIALS AND METHODS: Between March 1994 and September 2007, 740 consecutive patients (mean age, 75.7 y +/- 7.7; 69 women) underwent elective EVAR for infrarenal abdominal aortic aneurysm. Bivalirudin was used in 98 of these 740 (13.2%) and unfractioned heparin was used in the other 642 (86.8%). Complications were classified according to the Society of Vascular Surgery/International Society for Cardiovascular Surgery criteria. Major bleeding was defined as clinically overt blood loss resulting in a decrease of hemoglobin of more than 3 g/dL, any decrease in hemoglobin of more than 4 g/dL, transfusion of 2 U or more of red blood cells, or intracranial or retroperitoneal hemorrhage. RESULTS: Grade 1 major complications were observed in 161 of 642 patients (25.2%) in the heparin group and 12 of 98 patients (12.2%) in the bivalirudin group (P = .0046), whereas the incidences of grade 3 major complications were not significantly different between groups (P = .57). The rate of total complications was higher in the heparin group than in the bivalirudin group (247 of 642 [38.5%] vs 21 of 98 [21.4%]; P = .001). Major bleeding occurred in 10 of 98 patients (10.2%) receiving bivalirudin and in 91 of 642 patients (14.2%) receiving heparin (P = .34). One of 21 major complications (4.76%) in the bivalirudin group and 12 of 247 major complications (4.86%) in the heparin group were attributable to thrombosis (P = 1.0). CONCLUSIONS: Bivalirudin is a safe and feasible alternative to unfractionated heparin in patients undergoing EVAR.

The Road to Negative Behavior: Discriminatory Intentions in the German Population

This study analyzes discriminatory intentions shared by members of the German majority against several outgroups in Germany. Patterns of discriminatory intentions against various minority groups were investigated for several indicators, including gender, age, and political orientation, by means of a representative survey (N = 1,778). The relationship between prejudices and discriminatory intentions against different target groups was also analyzed. Prejudice and discriminatory intentions show moderate but consistently positive correlations in relation to one and the same target group. Moreover, it was found that discriminatory intentions against one outgroup are related to hostile attitudes towards other outgroups, too. The results support the hypothesis of a syndrome of group-focused enmity.

Social Factors Associated with Readiness for Sexual Activity in Adolescents: A Population-Based Cohort Study

Various factors are associated with sexual activity in adolescence and it is important to identify those that promote healthy and adaptive romantic and sexual development. The objectives of this study were to describe rates of early sexual intercourse (before 16 years) and sexual readiness in adolescence and to assess the extent to which these were social patterned. We prospectively studied nearly 5,000 15-year-olds from the Avon Longitudinal Study of Parents and Children, a UK birth cohort. Between 2006 and 2008, female and male participants answered a computer assisted interview about romantic and sexual behaviors in the last year. Predictors of sexual intercourse and readiness for sexual intercourse were examined across a range of sociodemographic measures. Overall, 17.7 % (95 % CI 16.7 %, 18.9 %) of participants reported having had sexual intercourse in the last year, with more girls than boys reporting sexual experience (risk ratio 1.30, 95 % CI 1.15, 1.47). Of these, one-third of both male and female were classed as unready because they were unwilling, lacking in autonomy, felt regret or had not used contraception. There was strong evidence of social patterning for sexual activity with higher rates for young people from poorer homes, with lower social class, and with younger, less educated mothers. In contrast, among 860 young people who had had sexual intercourse, there was no clear evidence of associations between social factors and sexual readiness. The lack of social patterning in sexual readiness supports the provision of comprehensive education to develop life skills for adolescents across all social groups.

Suicide assisted by right-to-die associations: a population based cohort study

Background: In Switzerland, assisted suicide is legal but there is concern that vulnerable or disadvantaged groups are more likely to die in this way than other people. We examined socio-economic factors associated with assisted suicide. Methods: We linked the suicides assisted by right-to-die associations during 2003–08 to a census-based longitudinal study of the Swiss population. We used Cox and logistic regression models to examine associations with gender, age, marital status, education, religion, type of household, urbanization, neighbourhood socio-economic position and other variables. Separate analyses were done for younger (25 to 64 years) and older (65 to 94 years) people. Results: Analyses were based on 5 004 403 Swiss residents and 1301 assisted suicides (439 in the younger and 862 in the older group). In 1093 (84.0%) assisted suicides, an underlying cause was recorded; cancer was the most common cause (508, 46.5%). In both age groups, assisted suicide was more likely in women than in men, those living alone compared with those living with others and in those with no religious affiliation compared with Protestants or Catholics. The rate was also higher in more educated people, in urban compared with rural areas and in neighbourhoods of higher socio-economic position. In older people, assisted suicide was more likely in the divorced compared with the married; in younger people, having children was associated with a lower rate. Conclusions: Assisted suicide in Switzerland was associated with female gender and situations that may indicate greater vulnerability such as living alone or being divorced, but also with higher education and higher socio-economic position.

Evaluating the disparity of female breast cancer mortality among racial groups - a spatiotemporal analysis

Background The literature suggests that the distribution of female breast cancer mortality demonstrates spatial concentration. There remains a lack of studies on how the mortality burden may impact racial groups across space and over time. The present study evaluated the geographic variations in breast cancer mortality in Texas females according to three predominant racial groups (non-Hispanic White, Black, and Hispanic females) over a twelve-year period. It sought to clarify whether the spatiotemporal trend might place an uneven burden on particular racial groups, and whether the excess trend has persisted into the current decade. Methods The Spatial Scan Statistic was employed to examine the geographic excess of breast cancer mortality by race in Texas counties between 1990 and 2001. The statistic was conducted with a scan window of a maximum of 90% of the study period and a spatial cluster size of 50% of the population at risk. The next scan was conducted with a purely spatial option to verify whether the excess mortality persisted further. Spatial queries were performed to locate the regions of excess mortality affecting multiple racial groups. Results The first scan identified 4 regions with breast cancer mortality excess in both non-Hispanic White and Hispanic female populations. The most likely excess mortality with a relative risk of 1.12 (p = 0.001) occurred between 1990 and 1996 for non-Hispanic Whites, including 42 Texas counties along Gulf Coast and Central Texas. For Hispanics, West Texas with a relative risk of 1.18 was the most probable region of excess mortality (p = 0.001). Results of the second scan were identical to the first. This suggested that the excess mortality might not persist to the present decade. Spatial queries found that 3 counties in Southeast and 9 counties in Central Texas had excess mortality involving multiple racial groups. Conclusion Spatiotemporal variations in breast cancer mortality affected racial groups at varying levels. There was neither evidence of hot-spot clusters nor persistent spatiotemporal trends of excess mortality into the present decade. Non-Hispanic Whites in the Gulf Coast and Hispanics in West Texas carried the highest burden of mortality, as evidenced by spatial concentration and temporal persistence.

Multiple independent genetic factors at NOS1AP modulate the QT interval in a multi-ethnic population.

Extremes of electrocardiographic QT interval are associated with increased risk for sudden cardiac death (SCD); thus, identification and characterization of genetic variants that modulate QT interval may elucidate the underlying etiology of SCD. Previous studies have revealed an association between a common genetic variant in NOS1AP and QT interval in populations of European ancestry, but this finding has not been extended to other ethnic populations. We sought to characterize the effects of NOS1AP genetic variants on QT interval in the multi-ethnic population-based Dallas Heart Study (DHS, n = 3,072). The SNP most strongly associated with QT interval in previous samples of European ancestry, rs16847548, was the most strongly associated in White (P = 0.005) and Black (P = 3.6 x 10(-5)) participants, with the same direction of effect in Hispanics (P = 0.17), and further showed a significant SNP x sex-interaction (P = 0.03). A second SNP, rs16856785, uncorrelated with rs16847548, was also associated with QT interval in Blacks (P = 0.01), with qualitatively similar results in Whites and Hispanics. In a previously genotyped cohort of 14,107 White individuals drawn from the combined Atherosclerotic Risk in Communities (ARIC) and Cardiovascular Health Study (CHS) cohorts, we validated both the second locus at rs16856785 (P = 7.63 x 10(-8)), as well as the sex-interaction with rs16847548 (P = 8.68 x 10(-6)). These data extend the association of genetic variants in NOS1AP with QT interval to a Black population, with similar trends, though not statistically significant at P<0.05, in Hispanics. In addition, we identify a strong sex-interaction and the presence of a second independent site within NOS1AP associated with the QT interval. These results highlight the consistent and complex role of NOS1AP genetic variants in modulating QT interval.

A spatial-temporal approach to surveillance of prostate cancer disparities in population subgroups

BACKGROUND: Prostate cancer mortality disparities exist among racial/ethnic groups in the United States, yet few studies have explored the spatiotemporal trend of the disease burden. To better understand mortality disparities by geographic regions over time, the present study analyzed the geographic variations of prostate cancer mortality by three Texas racial/ethnic groups over a 22-year period. METHODS: The Spatial Scan Statistic developed by Kulldorff et al was used. Excess mortality was detected using scan windows of 50% and 90% of the study period and a spatial cluster size of 50% of the population at risk. Time trend was analyzed to examine the potential temporal effects of clustering. Spatial queries were used to identify regions with multiple racial/ethnic groups having excess mortality. RESULTS: The most likely area of excess mortality for blacks occurred in Dallas-Metroplex and upper east Texas areas between 1990 and 1999; for Hispanics, in central Texas between 1992 and 1996: and for non-Hispanic whites, in the upper south and west to central Texas areas between 1990 and 1996. Excess mortality persisted among all racial/ethnic groups in the identified counties. The second scan revealed that three counties in west Texas presented an excess mortality for Hispanics from 1980-2001. Many counties bore an excess mortality burden for multiple groups. There is no time trend decline in prostate cancer mortality for blacks and non-Hispanic whites in Texas. CONCLUSION: Disparities in prostate cancer mortality among racial/ethnic groups existed in Texas. Central Texas counties with excess mortality in multiple subgroups warrant further investigation.

Population amalgamation and genetic variation: observations on artificially agglomerated tribal populations of Central and South America.

The interpretation of data on genetic variation with regard to the relative roles of different evolutionary factors that produce and maintain genetic variation depends critically on our assumptions concerning effective population size and the level of migration between neighboring populations. In humans, recent population growth and movements of specific ethnic groups across wide geographic areas mean that any theory based on assumptions of constant population size and absence of substructure is generally untenable. We examine the effects of population subdivision on the pattern of protein genetic variation in a total sample drawn from an artificial agglomerate of 12 tribal populations of Central and South America, analyzing the pooled sample as though it were a single population. Several striking findings emerge. (1) Mean heterozygosity is not sensitive to agglomeration, but the number of different alleles (allele count) is inflated, relative to neutral mutation/drift/equilibrium expectation. (2) The inflation is most serious for rare alleles, especially those which originally occurred as tribally restricted "private" polymorphisms. (3) The degree of inflation is an increasing function of both the number of populations encompassed by the sample and of the genetic divergence among them. (4) Treating an agglomerated population as though it were a panmictic unit of long standing can lead to serious biases in estimates of mutation rates, selection pressures, and effective population sizes. Current DNA studies indicate the presence of numerous genetic variants in human populations. The findings and conclusions of this paper are all fully applicable to the study of genetic variation at the DNA level as well.

Comparison of pain-resilient working individuals to population-based case controls with/without momentary low back pain

Background: Few studies have examined the 20% of individuals who never experience an episode of low back pain (LBP). To date, no investigation has been undertaken that examines a group who claim to have never experienced LBP in their lifetime in comparison to two population-based case–control groups with and without momentary LBP. This study investigates whether LBP-resilient workers between 50 and 65 years had better general health, demonstrated more positive health behaviour and were better able to achieve routine activities compared with both case–control groups. Methods: Forty-two LBP-resilient participants completed the same pain assessment questionnaire as a population-based LBP sample from a nationwide, large-scale cross-sectional survey in Switzerland. The LBP-resilient participants were pairwise compared to the propensity score-matched case controls by exploring differences in demographic and work characteristics, and by calculating odds ratios (ORs) and effect sizes. A discriminant analysis explored group differences, while the multiple logistic regression analysis specified single indicators which accounted for group differences. Results: LBP-resilient participants were healthier than the case controls with momentary LBP and achieved routine activities more easily. Compared to controls without momentary LBP, LBP-resilient participants had a higher vitality, a lower workload, a healthier attitude towards health and behaved more healthily by drinking less alcohol. Conclusions: By demonstrating a difference between LBP-resilient participants and controls without momentary LBP, the question that arises is what additional knowledge can be attained. Three underlying traits seem to be relevant about LBP-resilient participants: personality, favourable work conditions and subjective attitudes/attributions towards health. These rationales have to be considered with respect to LBP prevention.

The association of genetic groups 1, 2, and 3 of Mycobacterium tuberculosis with pulmonary and extra-pulmonary tuberculosis

Objective. To investigate the association of the three major genetic groups of Mycobacterium tuberculosis with pulmonary and extra-pulmonary tuberculosis in clustered and non-clustered TB cases in the Houston area. ^ Study design. Secondary analysis of an ambi-directional study. ^ Study population. Three hundred fifty-eight confirmed cases of tuberculosis in the Houston that occurred between October 1995 and May 1997, who had been interviewed by the Houston T13 Initiative staff at Baylor College of Medicine, and whose isolates have had their DNA fingerprint and genetic group determined. ^ Exclusions. Individuals whose mycobacterial genotype was unknown, or whose data variables were unavailable. ^ Source of data. Laboratory results, patient interviews, and medical records at clinics and hospitals of the study population. ^ Results. In clustered cases, the majority of both, pulmonary and extra-pulmonary TB cases were caused by genetic group 1. Independent factors were assessed to determine the interactions that may influence the site of infection or increase the risk for one site or another. HIV negative males were protected against extra-pulmonary TB compared to HIV negative females. Individuals ages 1–14 years were at higher risk of having extra-pulmonary TB. Group 3 organisms were found less frequently in the total population in general, especially in extra-pulmonary disease. This supports the evidence in previous studies that this group is the least virulent and genetically distinct from the other two groups. Group 1 was found more frequently among African Americans than other ethnic groups, a trend for future investigations. ^ Among the non-clustered cases, group 2 organisms were the majority of the organisms found in both sites. They were also the majority of organisms found in African Americans, Caucasians, and Hispanics causing the majority of the infections at both sites. However, group 1 organisms were the overwhelming majority found in Asian/Pacific Islander individuals, which may indicate these organisms are either endemic to that area, or that there is an ethnic biological factor involved. This may also be due to a systematic bias, since isolates from individuals from that geographic region lack adequate copies of the insertion sequence IS6110, which leads to their placement in the non-clustered population. ^ The three genetic groups of Mycobacterium tuberculosis were not found equally distributed between sites of infection in both clustered and non-clustered cases. Furthermore, these groups were not distributed in the same patterns among the clustered and non-clustered cases, but rather in distinct patterns. ^

Twenty-three per cent of the Swiss adult population are using complementary medicine

Aim of the study: This study investigated the use among the Swiss adult population and the regional dissemination in Switzerland of various methods of complementary medicine (CM). It focused on CM methods that required visiting a physician or therapist and excluded e.g. over-the-counter drugs. Data and Methods: Data of the Swiss Health Survey 2007 were obtained from the Swiss Federal Statistical Office. This survey is performed every 5 years in a sample and is representative of the Swiss resident population from the age of 15 on. It consists of a telephone interview followed by a written questionnaire (2007: 18'760 and 14'432 respondents, respectively) and includes questions about people's state of health, general living conditions, lifestyle, health insurance and usage of health services. Users and non-users of CM were compared using logistic regression models. Results: 23.0 % of the Swiss adult population (women: 30.5 %, men: 15.2 %) used CM during the 12 months before the survey. Homeopathy (6.4 %), osteopathy (5.4 %) and acupuncture (4.9 %) were the most popular methods. The average number of treatments within 12 months for these three methods was 3.1 ± 3.6, 3.5 ± 3.3 and 6.6 ± 5.8, respectively. For treatments with homeopathy and acupuncture, medical practitioners were more commonly consulted than non-medical practitioners, for treatments with osteopathy no difference was found. By means of logistic regression, CM users and non-users were compared. There were significant differences in the use of CM between genders, age groups, levels of education and areas of living. Women, people aged 25 to 64 years, and people with higher levels of education used CM more commonly than men, people below 25 or above 64 years of age, or those with poorer education. Lake Geneva region and central Switzerland had a higher proportion of CM users than the other regions. Discussion: Almost one fourth of the Swiss adult population had used CM within 12 months before the survey. User profiles were comparable to those in other countries. Despite a generally lower self-perceived health status, elderly people were less likely to use CM. Reference: Klein SD, Frei-Erb M, Wolf U. Usage of complementary medicine across Switzerland. Results of the Swiss Health Survey 2007. Swiss Med Wkly. 2012;142:w13666.

Twenty-three per cent of the Swiss adult population are using complementary medicine

Aim of the study Various forms of complementary medicine (CM) play an important role in the Swiss health care system, they are appreciated by a majority of the population and mostly used complementarily rather than alternatively to conventional medicine. This study investigates, how many people in Switzerland are actually being treated with CM, and what the most popular methods of CM are. Data Data of the Swiss Health Survey 2007 were obtained from the Swiss Federal Statistical Office. This survey is performed every 5 years amongst a sample of the Swiss resident population above 15 years of age. It consists of a telephone interview followed by a written questionnaire (2007: 18'760 and 14'432 respondents, respectively) and includes questions about people's state of health, general living conditions, lifestyle, health insurance and usage of health services. Results 23.0% of the Swiss adult population (women: 30.5%, men: 15.2%) used CM during the 12 months before the survey. Homeopathy (6.4%), osteopathy (5.4%) and acupuncture (4.9%) were the most popular methods. The average number of treatments within 12 months for these three methods was 3.1, 3.5 and 6.6, respectively. For treatments with homeopathy and acupuncture, medical practitioners were more commonly consulted than non-medical practitioners, for treatments with osteopathy no difference was found. By means of logistic regression, CM users and non-users were compared. There were significant differences in the use of CM between genders, age groups, levels of education and areas of living. Women, people aged 25 to 64 years, and people with higher education used CM more commonly than men, people below 25 or above 64 years of age, or those with poorer education. Lake Geneva region and central Switzerland had a higher proportion of CM users than the other regions. Discussion While 2 years ago, 67.0% of the Swiss population approved a referendum in favour of CM, we find that 23.0% are in fact using it. Current political discussions focus on effectiveness, cost effectiveness and suitability of CM to decide which methods should be permanently covered by the basic health insurance.

Discrete Improvement in Racial Disparity in Survival among Patients with Stage IV Colorectal Cancer: a 21-Year Population-Based Analysis

Purpose Recently, multiple clinical trials have demonstrated improved outcomes in patients with metastatic colorectal cancer. This study investigated if the improved survival is race dependent. Patients and Methods Overall and cancer-specific survival of 77,490 White and Black patients with metastatic colorectal cancer from the 1988–2008 Surveillance Epidemiology and End Results registry were compared using unadjusted and multivariable adjusted Cox proportional hazard regression as well as competing risk analyses. Results Median age was 69 years, 47.4 % were female and 86.0 % White. Median survival was 11 months overall, with an overall increase from 8 to 14 months between 1988 and 2008. Overall survival increased from 8 to 14 months for White, and from 6 to 13 months for Black patients. After multivariable adjustment, the following parameters were associated with better survival: White, female, younger, better educated and married patients, patients with higher income and living in urban areas, patients with rectosigmoid junction and rectal cancer, undergoing cancer-directed surgery, having well/moderately differentiated, and N0 tumors (p<0.05 for all covariates). Discrepancies in overall survival based on race did not change significantly over time; however, there was a significant decrease of cancer-specific survival discrepancies over time between White and Black patients with a hazard ratio of 0.995 (95 % confidence interval 0.991–1.000) per year (p=0.03). Conclusion A clinically relevant overall survival increase was found from 1988 to 2008 in this population-based analysis for both White and Black patients with metastatic colorectal cancer. Although both White and Black patients benefitted from this improvement, a slight discrepancy between the two groups remained.